Simulate.  Analyze.  Explore.  High performance, high usability toolkits for  predictive biomolecular simulation.

 

Simulation & Setup

OpenMM

OpenMM is CPU / GPU accelerated molecular dynamics with an intuitive Python interface.  Wrappers for C, C++, and Fortran.

YANK

YANK is a GPU-accelerated Python framework for exploring algorithms for alchemical free energy calculations.

PDBFixer

A powerful, flexible tool for preparing PDB files for molecular simulation or modeling, capable of running in interactive, Python-scriptable, or fully automated modes.

Ensembler

Ensembler is an automated pipeline for generating diverse arrays of protein configurations from omics-scale genomic and structural data.

Analysis & Exploration

MDTraj

Easy-to-use trajectory readers for almost every simulation format imaginable.  Read, write, and analyze trajectories with only a few lines of Python code.

PyEMMA

PyEMMA: Markov models and rate models from MD simulations. Accurate and extensive tools for estimation, validation, analysis and visualization.

MSMBuilder

MSMBuilder creates kinetic rate models from multiple simulations.  Parallelizes the molecular simulation problem and enables direct comparison to experiment.



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